The 3gb cards have about 10% less Cuda cores than the 6gb one
The 6gb is over locked a little so you’ll probably get around 15% difference at most in FPS
The main draw I think would be the vram
The 6 GB is decently faster around 15%but the real benefit is it's extra Vram which allows it to perform better with higher resolutions and games with alot of textures. I wouldn't get the 3 GB card personally.
there is about a 10% performance hit on the 1060 3GB from the 6GB. But if you find yourself using more than your allotted 3GB of VRAM, the performance hit would be significantly more than that.